Presentation on theme: "Barcode Wales: DNA barcoding the flora of Wales"— Presentation transcript:
1 Barcode Wales: DNA barcoding the flora of Wales Natasha de Vere, Tim Rich, Col Ford, Sarah Trinder, Charlie Long, Chris Moore, Danielle Satterthwaite, Helena Davies, Joe Moughan, Addie Griffith, Laura Jones, Joel Allainguillaume, Mike Wilkinson, Kevin Walker, Tatiana Tatarinova, Hannah Garbett, Les Baillie, Jenny Hawkins
2 DNA barcoding DNA based species identification Once reference barcodes are established will always be able to identify that speciesInternationally agreed regions of DNA used: rbcL & matK for plantsOpen science>Cotoneaster_cambricusAGAGACTAAAGCAAGTGTTGGATTCAAAGCTGGTGTTAAAGATTATAAATTGACTTATTATACTCCTGACTATGAAACCAAAGATACTGATATTTTGGCAGCATTTCGAGTAACTCCTCAACCTGGAGTTCCACCTGAGGAAGCAGGGGCCGCGGTAGCTGCTGAATCTTCTACTGGTACATGGACAACTGTATGGACTGACGGTCTTACCAGTCTTGATCGTTACAAAGGTCGATGCTACCACATCGAGCCTGTTGCTGGAGAAGAAAGTCAATTTATTGCTTATGTAGCTTACCCCTTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCCATTGTAGGTAATGTGTTTGGGTTCAAGGCCCTGCGCGCTCTACGTCTGGAGGATTTGCGAATCCCTACTGCTTATGTTAAAACTTTCCAGGGCCCGCCTCATGGTATCCAAGTTGAGAGAGATAAATTGAACAAGTATGGCCGCCCTCTATTGGGATGTACTATAAAACCAAAATTGGGGTTATCCGCTAAGAATTACGGTAGAGCAGTTTATGAATGTC
3 What pollen is it carrying? What do they eat?What’s in this?What pollen is it carrying?Is this legal?
4 Barcode Wales: Cod Bar Cymru DNA barcode the native flowering plants and conifers of WalesDevelop applications that utilise this research platform
5 Sample collection 1143 native flowering plants and conifers 4272 individuals sampled, 3637 herbarium, 635 freshly collectedAll specimens verified by taxonomic expertHerbarium vouchers and full collection details for all samples
6 DNA barcoding protocol DNA extraction: Qiagen kits, modified for herbarium materialAmplification: rbcL 5 & matK 23 primer combinationsSanger sequencingManual editing, multiple alignmentSequences uploaded onto BOLD & GenBank – publically available
7 de Vere N, Rich TCG, Ford CR, Trinder SA, Long C, et al de Vere N, Rich TCG, Ford CR, Trinder SA, Long C, et al. (2012) DNA Barcoding the Native Flowering Plants and Conifers of Wales. PLoS ONE 7(6): e37945.
8 RecoverabilityrbcLmatKrbcL & matKNo. of spp. sequenced (1143)1117 (98%)1031 (90%)1025 (90%)No. of spp. with > 1 individual sequenced1041 (91%)814 (71%)808 (71%)Mean no. of individuals per spp.32Mode of individuals per spp.Range of individuals per spp.1 - 91 - 8Total no. of individuals sequenced330424192349In total 5,723 barcode sequences obtained for the 1143 species
9 Effect of herbarium specimen age Spearman Rank Correlation:rbcL rho = 0.993***matK rho = 0.986***
10 Relative discrimination 808 species with multiple individuals sequenced for both rbcL & matK6999751006898749956965795
11 rbcL & matK discrimination ScalenMean discrimination % (SD)10x10 km25382 (3)2x2 km111693 (6)Species lists generated for each square, discrimination assessed by presence of a barcode gap
12 Roots, shoots and pollen Root analysisIdentification at single pollen grain resolutionIdentification of pollen productsGives a feeling “of Youthful Exuberance!”
13 Honey and drug discovery Collect honey from throughout the UK.Test antibacterial properties of honey against MRSA and Clostridium difficile.DNA barcode honey using next generation DNA sequencing (454).Identify plant derivedphytochemicals that increase antimicrobial activity.
16 DNA barcoding and phylogenetics ML tree for rbcL,RAxML (GTR+CAT)1000 bootstraps, on the CIPRES supercomputer cluster56% of species form monophyletic groups44% with bootstrap support >70%
17 DNA barcoding and phylogenetic ecology ML tree for rbcL, threatened species traced using Mesquite
18 What’s next? Barcode UK Barcode Alien Phylogeny for the UK flora Development of bioinformatic toolsDiet analysis of endangered speciesPollinator services
19 Thank you!Funding from Welsh Government, National Botanic Garden of Wales, National Museum Wales, Countryside Council for WalesSponsorship from the people of WalesScience at the Garden of Wales on Facebook